Regulation of gene expression is achieved by the direct and/or indirect interaction of regulatory proteins such as transcription factors with cis-acting DNA regulatory regions, including promoters, promoter elements, and promoter motifs, which may be located upstream, downstream and/or within a gene of interest. Certain regulatory proteins can interact with regulatory regions for a number of genes, often driving the coordinate expression of multiple genes in a pathway. For example, binding of a transcription factor to a promoter or promoter element usually results in a modulation (e.g., an increase) of basal rates of transcription initiation and/or elongation. Promoters typically have a modular organization that includes multiple cis-elements (promoter elements), which can interact in additive or synergistic manners to modulate transcription, e.g., to result in constitutive or non-constitutive expression patterns. Non-constitutive expression patterns can include tissue-specific expression, developmental stage-specific expression, and environmental factor-specific expression.
Identification of regulatory proteins that bind to particular DNA regulatory regions can provide tools to facilitate the selective expression of proteins of interest, e.g., to modify plant biosynthetic pathways and/or to modify plant responses to environmental stress and disease conditions.